Re: [HCP-Users] The minimal preprocessing pipelines for HCP
Thank you for your explanation. I have a little bit confused. As the third way of registration you mentioned, why could we simply apply the motion correction for fMRI volume data and align to T1 image with bbr, then project to fs32k native surface as one step registration, couldn't we? If not, how was this motion correction warpfield for each fMRI volume involved in current registration pipeline (native volume -- MNI space -- template surface)? Did I miss something? Best, Ting On Mon, Mar 2, 2015 at 9:52 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: This is a good point and something we thought about at the time. The reason we did it this way was to avoid having to generate two separate volume timeseries files (making these is by far the most time-consuming part of the fMRIVolume pipeline). We would have had to make one that was fully distortion corrected, but put into native T1w space with a single resampling step and another (the only one that we currently make) that is put into MNI space with a single resampling step. There was a third way this could have been done (much more complicated, but without the single spline interpolation step in the volume): We could have applied the volume warpfield for each fMRI timeseries volume to the native mesh surfaces to make many copies of them (because of the motion correction there is a unique warpfield for each fMRI volume) and resampled onto the surfaces directly from the original fMRI timeseries. This also would have been more exact because while volumes must be resampled after registration to a voxel grid, surfaces can have the transformations applied to their vertex coordinate positions exactly (in mm). Coding this up would have been a bit of a challenge (and slower), as things like the high local COV exclusion expect the surface not to move around and thus would also have to be computed for every fMRI volume. Perhaps if computers get faster and someone gets bored enough to bother, this will get implemented… Peace, Matt. From: ting xu xutin...@gmail.com Date: Monday, March 2, 2015 at 8:30 PM To: Matt Glasser glass...@wusm.wustl.edu Subject: The minimal preprocessing pipelines for HCP Dear Dr. Glasser, My name is Ting Xu and I am a postdoc from Nathan Kline Institute, New York state. I am writing to enquire about the order of preprocess steps in HCP pipeline. I read the pipeline scripts and noticed that the order of preprocess for surface data is (1) registered native volume to MNI volume using fnirt, (2) applied the fnirt registration to native surface, (3) project data from volume to surface in MNI space, (4) registered the data to fs32k template. There is another way for registration, e.g. project the data from native volume to native surface then register to fs32k template. I was wondering why should we bring the the data to MNI space for both native volume and surface first, and then do the projection in MNI space? Would you please tell me are there any specific reasons behind this? Many thanks for your comments! Warmly regards, Ting -- Xu,Ting Postdoc Nathan Kline Institute, Child Mind Institute Laboratory for Functional Connectome and Development (LFCD), Institute of Psychology, CAS -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Headshape data in HCP-MEG II release
Hi Denis Let me CC this also to the HCP-users email list, where others might also learn something from it. For the MEG1 release we had planned and documented that we would include the hs_file. But then we realized that 1) it has facial details in it (nose and around eyes), which we had agreed in general not to release for identification reasons 2) the high-res T1 anatomical MRIs that are released do not cover the full head and are anyway defaced So in the MEG1 release we already excldued the hs_file from release and in the MEG2 release wel also updated the documentation. The MEG1 documentation is incorrect as it mentions the hs_file in the list of released files. Important to note is that the data that we share in the anatomy package is already coregistered by means of an additional full head (not only brain) T1 scan that we made specifically for the MEG coregistration. So for each subject we match the hs_file to the (scalp and face optimized) full-head MEG specific T1, which we match to the (brain optimized) high-res defaced T1. The full-head MEG specific T1 is not shared, only the high-res defaced T1 is shared. That means that with the released/downloadable data you are not able to replicate the coregistration procedure to the level of accuracy that we have been able to do it with the unreleased T1 data. So you’ll just have to trust us on the coregistration. All coregistration details are shared in the SUBJID_MEG_anatomy_transform.txt text file. I hope those serve the needs of your analysis pipeline. If not, let us know. In case you need a stub file for the pipeline, you can find a hs_file on http://figshare.com/account/projects/3629. It is one from a non-HCP subject that was not recorded at the SLU MEG centre, but it should have the same format. best regards, Robert On 28 Feb 2015, at 15:30, Denis-Alexander Engemann denis.engem...@gmail.com wrote: Hi Robert, I'm currently working on MNE-Python support for the HCP data. Having read the manuals and downloaded the unprocessed and processed MEG data, I realised that the hs_file has apparently been removed from relase I to release II. I also could not find the head shape data in any other matfile. Greping the megconnectome code it seems the pipeline code expects these files and is also supposed to write mat files with the head shape information. Unfortunately, without the head shape MNE-Python cannot be used with the HCP data as is. I'm wondering if I've missed something. Any hint would be appreciated. Best, Denis ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)
It isn't impossible to get the data into the grayordinate space we use, though the volume to surface mapping part could be problematic because of alignment/group average issues. As long as the data is nonlinearly registered to MNI152 space, you are really only missing the volume subcortical label file to be able to create a cifti file in our grayordinate space. I think you can get this file by downloading a single subject's dataset from connectomedb (download images, structural preprocessed?). There will be an enhancement added to wb_command that will allow you to create this volume label file from an existing cifti file, rather than downloading it. Tim On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma maxxx...@umn.edu wrote: Thank you for your suggestion Dr. Harms. It seems that it is the only way to compare subcortical networks at this moment. On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael mha...@wustl.edu wrote: Not sure if this will help your purposes, but the HCP500-PTN (Parcellation+Timeseries+Netmats) distribution includes the following: melodic_IC_sum.nii.gz: ICA spatial maps projected from the surface into the volume, for reporting purposes. MNI152 space. I don't think we have any group ICA maps derived originally in the volume space since the group ICA was done using the FIX-cleaned CIFTI time series as inputs. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 10:23 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Thank you for your reply Dr. Glasser. I've read this recommendation elsewhere on the forum and your point is well taken. Yet in our case the purpose is a bit different. We are not trying to do any analysis but to compare the HCP ICA maps with classical maps that have been generated in the volumetric space. Although this may not be accurate, it'll offer us some insight into the HCP maps. On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would recommend mapping your individual subject data onto individual subject surfaces and then registering on the surface. Volume to surface mapping onto a group average surface from a group average volume is not particularly accurate in comparison. Once you average cortical data in the volume, you lose the ability to do accurate spatial localization to cortical areas. Instead data can be easily mapped onto locations centimeters away in 2D from the correct location on the folded cortical sheet. Also, group average surfaces are very blurry in many cortical regions because different people have different folding patterns that cannot be registered (e.g. some people can have two gyri where others have only one). Thus, it’s really better to do your cortical analysis on the surface to begin with, as we do in the HCP with CIFTI. Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 at 9:27 PM To: Timothy Coalson tsc...@mst.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Hi, I am still looking forward to getting help on this issue. Is an Atlas_ROIs.2.nii.gz or similar files provided for volume to surface mapping onto R440 group template? If not, will there be any in the future? Thanks, Cherry ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this
Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)
Hi Timothy, Thank you for your reply. So sounds like that the file Atlas_ROIs.2.nii.gz for whichever subject can get me the same result? I'd also like to follow up on Dr. Harms' suggestion on using melodic_IC_sum.nii.gz. Given the discussion on the inaccuracy in group level surface/volume mapping, it seems that melodic_IC_sum.nii.gz is not an accurate representation of the HCP maps in the MNI space, thus it is for reporting purposes? Thanks, Cherry On Tue, Mar 3, 2015 at 7:06 PM, Timothy Coalson tsc...@mst.edu wrote: It isn't impossible to get the data into the grayordinate space we use, though the volume to surface mapping part could be problematic because of alignment/group average issues. As long as the data is nonlinearly registered to MNI152 space, you are really only missing the volume subcortical label file to be able to create a cifti file in our grayordinate space. I think you can get this file by downloading a single subject's dataset from connectomedb (download images, structural preprocessed?). There will be an enhancement added to wb_command that will allow you to create this volume label file from an existing cifti file, rather than downloading it. Tim On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma maxxx...@umn.edu wrote: Thank you for your suggestion Dr. Harms. It seems that it is the only way to compare subcortical networks at this moment. On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael mha...@wustl.edu wrote: Not sure if this will help your purposes, but the HCP500-PTN (Parcellation+Timeseries+Netmats) distribution includes the following: melodic_IC_sum.nii.gz: ICA spatial maps projected from the surface into the volume, for reporting purposes. MNI152 space. I don't think we have any group ICA maps derived originally in the volume space since the group ICA was done using the FIX-cleaned CIFTI time series as inputs. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 10:23 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Thank you for your reply Dr. Glasser. I've read this recommendation elsewhere on the forum and your point is well taken. Yet in our case the purpose is a bit different. We are not trying to do any analysis but to compare the HCP ICA maps with classical maps that have been generated in the volumetric space. Although this may not be accurate, it'll offer us some insight into the HCP maps. On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would recommend mapping your individual subject data onto individual subject surfaces and then registering on the surface. Volume to surface mapping onto a group average surface from a group average volume is not particularly accurate in comparison. Once you average cortical data in the volume, you lose the ability to do accurate spatial localization to cortical areas. Instead data can be easily mapped onto locations centimeters away in 2D from the correct location on the folded cortical sheet. Also, group average surfaces are very blurry in many cortical regions because different people have different folding patterns that cannot be registered (e.g. some people can have two gyri where others have only one). Thus, it’s really better to do your cortical analysis on the surface to begin with, as we do in the HCP with CIFTI. Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 at 9:27 PM To: Timothy Coalson tsc...@mst.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Hi, I am still looking forward to getting help on this issue. Is an Atlas_ROIs.2.nii.gz or similar files provided for volume to surface mapping onto R440 group template? If not, will there be any in the future? Thanks, Cherry ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the
Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)
A better way to put it is any volume-based group average cortical result is not an accurate representation of the underlying subjects’ data. The results that Mike was talking about are generated by taking the group CIFTI ICA results and dual regressing them into each individual’s CIFTI dense timeseries (for stage one of dual regression) and then the resulting individual subject component timecourses into each subject’s volume timeseries to make individual subject component spatial maps in the volume. This is accurate as far as getting individual subject volume maps (because we don’t apply any volume-based smoothing), however as soon as you try to average these maps across subjects (to create melodic_IC_sum.nii.gz) you aren’t aligning like with like any more and hence get an inaccurate result. Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Tuesday, March 3, 2015 at 7:15 PM To: Timothy Coalson tsc...@mst.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Hi Timothy, Thank you for your reply. So sounds like that the file Atlas_ROIs.2.nii.gz for whichever subject can get me the same result? I'd also like to follow up on Dr. Harms' suggestion on using melodic_IC_sum.nii.gz. Given the discussion on the inaccuracy in group level surface/volume mapping, it seems that melodic_IC_sum.nii.gz is not an accurate representation of the HCP maps in the MNI space, thus it is for reporting purposes? Thanks, Cherry On Tue, Mar 3, 2015 at 7:06 PM, Timothy Coalson tsc...@mst.edu wrote: It isn't impossible to get the data into the grayordinate space we use, though the volume to surface mapping part could be problematic because of alignment/group average issues. As long as the data is nonlinearly registered to MNI152 space, you are really only missing the volume subcortical label file to be able to create a cifti file in our grayordinate space. I think you can get this file by downloading a single subject's dataset from connectomedb (download images, structural preprocessed?). There will be an enhancement added to wb_command that will allow you to create this volume label file from an existing cifti file, rather than downloading it. Tim On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma maxxx...@umn.edu wrote: Thank you for your suggestion Dr. Harms. It seems that it is the only way to compare subcortical networks at this moment. On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael mha...@wustl.edu wrote: Not sure if this will help your purposes, but the HCP500-PTN(ParcellationTimeseriesNetmats)distribution includes the following: melodic_IC_sum.nii.gz: ICA spatial maps projected from the surface into the volume, for reporting purposes. MNI152 space. I don't think we have any group ICA maps derived originally in the volume space since the group ICA was done using the FIX-cleaned CIFTI time series as inputs. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 10:23 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum) Thank you for your reply Dr. Glasser. I've read this recommendation elsewhere on the forum and your point is well taken. Yet in our case the purpose is a bit different. We are not trying to do any analysis but to compare the HCP ICA maps with classical maps that have been generated in the volumetric space. Although this may not be accurate, it'll offer us some insight into the HCP maps. On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would recommend mapping your individual subject data onto individual subject surfaces and then registering on the surface. Volume to surface mapping onto a group average surface from a group average volume is not particularly accurate in comparison. Once you average cortical data in the volume, you lose the ability to do accurate spatial localization to cortical areas. Instead data can be easily mapped onto locations centimeters away in 2D from the correct location on the folded cortical sheet. Also, group average surfaces are very blurry in many cortical regions because different people have different folding patterns that cannot be registered (e.g. some people can have two gyri where others have only one). Thus, it’s really better to do your cortical analysis on the surface to begin with, as we do in the HCP with CIFTI. Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Sunday,
